I am relatively new to bioinformatics and especially in working with next generation sequencing data. I am working on a study that aims to identify polymorphisms that are associated with a certain phenotype. I intend to do this through bulk segregant analysis where I have whole genome sequences of two bulks, each comprising 10 individuals. The aim is to determine allele frequencies in order to try and determine any association with the phenotype. I am not sure how to proceed! Can someone kindly advise me on how this is done and which software I can use (preferably one that is not command line based). I have been using CLC Workbench but it seems like it has limitations in conducting this type of analysis. Any help will be greatly appreciated.
Thanks a lot. I have used GALAXY before for variant detection and so I will explore it further to see how analysis on allele frequency can be done. I will also explore CLC further as it seems I am not familiar with functionality for conducting this kind of analysis. Thanks.